Mon 24 Dec 07:52:43 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2opl-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2opl-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2opl-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opl-4.0-parrot-noncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opl-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opl-4.0-parrot-noncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 07:52:48 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opl-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opl-4.0-parrot-noncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 231 and 0 Target number of residues in the AU: 231 Target solvent content: 0.6652 Checking the provided sequence file Detected sequence length: 187 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 374 Adjusted target solvent content: 0.46 Input MTZ file: 2opl-4.0-parrot-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 47.200 82.950 95.370 90.000 90.000 90.000 Input sequence file: 2opl-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 2992 target number of atoms Had to go as low as 0.75 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 62.588 4.000 Wilson plot Bfac: 88.38 3418 reflections ( 99.19 % complete ) and 0 restraints for refining 3299 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3542 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3500 (Rfree = 0.000) for 3299 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.95 4.17 Search for helices and strands: 0 residues in 0 chains, 3358 seeds are put forward NCS extension: 0 residues added, 3358 seeds are put forward Round 1: 115 peptides, 23 chains. Longest chain 8 peptides. Score 0.288 Round 2: 158 peptides, 27 chains. Longest chain 10 peptides. Score 0.406 Round 3: 186 peptides, 30 chains. Longest chain 10 peptides. Score 0.468 Round 4: 183 peptides, 25 chains. Longest chain 14 peptides. Score 0.539 Round 5: 195 peptides, 26 chains. Longest chain 19 peptides. Score 0.565 Taking the results from Round 5 Chains 26, Residues 169, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 6238 restraints for refining 2702 atoms. 5530 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2967 (Rfree = 0.000) for 2702 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 2: After refmac, R = 0.2504 (Rfree = 0.000) for 2661 atoms. Found 12 (12 requested) and removed 30 (6 requested) atoms. Cycle 3: After refmac, R = 0.2498 (Rfree = 0.000) for 2608 atoms. Found 10 (12 requested) and removed 18 (6 requested) atoms. Cycle 4: After refmac, R = 0.2310 (Rfree = 0.000) for 2592 atoms. Found 10 (12 requested) and removed 16 (6 requested) atoms. Cycle 5: After refmac, R = 0.2261 (Rfree = 0.000) for 2569 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 3.90 Search for helices and strands: 0 residues in 0 chains, 2663 seeds are put forward NCS extension: 37 residues added (0 deleted due to clashes), 2700 seeds are put forward Round 1: 156 peptides, 30 chains. Longest chain 12 peptides. Score 0.342 Round 2: 168 peptides, 27 chains. Longest chain 13 peptides. Score 0.448 Round 3: 173 peptides, 26 chains. Longest chain 13 peptides. Score 0.485 Round 4: 191 peptides, 26 chains. Longest chain 24 peptides. Score 0.551 Round 5: 166 peptides, 26 chains. Longest chain 16 peptides. Score 0.458 Taking the results from Round 4 Chains 28, Residues 165, Estimated correctness of the model 0.0 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 6077 restraints for refining 2700 atoms. 5369 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2530 (Rfree = 0.000) for 2700 atoms. Found 12 (12 requested) and removed 41 (6 requested) atoms. Cycle 7: After refmac, R = 0.2317 (Rfree = 0.000) for 2646 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 8: After refmac, R = 0.2312 (Rfree = 0.000) for 2615 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 9: After refmac, R = 0.2165 (Rfree = 0.000) for 2596 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 10: After refmac, R = 0.1623 (Rfree = 0.000) for 2587 atoms. Found 2 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.76 3.97 Search for helices and strands: 0 residues in 0 chains, 2662 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 2692 seeds are put forward Round 1: 146 peptides, 29 chains. Longest chain 10 peptides. Score 0.315 Round 2: 186 peptides, 32 chains. Longest chain 12 peptides. Score 0.434 Round 3: 184 peptides, 33 chains. Longest chain 19 peptides. Score 0.408 Round 4: 195 peptides, 31 chains. Longest chain 19 peptides. Score 0.486 Round 5: 196 peptides, 26 chains. Longest chain 21 peptides. Score 0.569 Taking the results from Round 5 Chains 28, Residues 170, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 5975 restraints for refining 2701 atoms. 5270 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2336 (Rfree = 0.000) for 2701 atoms. Found 12 (12 requested) and removed 38 (6 requested) atoms. Cycle 12: After refmac, R = 0.2325 (Rfree = 0.000) for 2639 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 13: After refmac, R = 0.1687 (Rfree = 0.000) for 2619 atoms. Found 3 (12 requested) and removed 10 (6 requested) atoms. Cycle 14: After refmac, R = 0.2028 (Rfree = 0.000) for 2594 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 15: After refmac, R = 0.1667 (Rfree = 0.000) for 2588 atoms. Found 11 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.74 3.95 Search for helices and strands: 0 residues in 0 chains, 2699 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 2730 seeds are put forward Round 1: 150 peptides, 31 chains. Longest chain 8 peptides. Score 0.295 Round 2: 175 peptides, 30 chains. Longest chain 12 peptides. Score 0.424 Round 3: 184 peptides, 30 chains. Longest chain 16 peptides. Score 0.460 Round 4: 183 peptides, 27 chains. Longest chain 15 peptides. Score 0.506 Round 5: 182 peptides, 27 chains. Longest chain 14 peptides. Score 0.503 Taking the results from Round 4 Chains 28, Residues 156, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 6143 restraints for refining 2702 atoms. 5520 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2110 (Rfree = 0.000) for 2702 atoms. Found 6 (12 requested) and removed 21 (6 requested) atoms. Cycle 17: After refmac, R = 0.2239 (Rfree = 0.000) for 2667 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 18: After refmac, R = 0.2122 (Rfree = 0.000) for 2657 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 19: After refmac, R = 0.1684 (Rfree = 0.000) for 2638 atoms. Found 3 (12 requested) and removed 10 (6 requested) atoms. Cycle 20: After refmac, R = 0.1565 (Rfree = 0.000) for 2628 atoms. Found 6 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.78 3.99 Search for helices and strands: 0 residues in 0 chains, 2685 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 2708 seeds are put forward Round 1: 134 peptides, 27 chains. Longest chain 9 peptides. Score 0.298 Round 2: 150 peptides, 26 chains. Longest chain 11 peptides. Score 0.391 Round 3: 153 peptides, 24 chains. Longest chain 13 peptides. Score 0.440 Round 4: 160 peptides, 25 chains. Longest chain 13 peptides. Score 0.451 Round 5: 173 peptides, 25 chains. Longest chain 18 peptides. Score 0.502 Taking the results from Round 5 Chains 25, Residues 148, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 6367 restraints for refining 2702 atoms. 5800 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2192 (Rfree = 0.000) for 2702 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 22: After refmac, R = 0.2433 (Rfree = 0.000) for 2670 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Cycle 23: After refmac, R = 0.2152 (Rfree = 0.000) for 2645 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 24: After refmac, R = 0.2188 (Rfree = 0.000) for 2627 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 25: After refmac, R = 0.2008 (Rfree = 0.000) for 2611 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 3.96 Search for helices and strands: 0 residues in 0 chains, 2702 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 2729 seeds are put forward Round 1: 118 peptides, 25 chains. Longest chain 9 peptides. Score 0.261 Round 2: 125 peptides, 25 chains. Longest chain 9 peptides. Score 0.295 Round 3: 119 peptides, 23 chains. Longest chain 11 peptides. Score 0.307 Round 4: 122 peptides, 20 chains. Longest chain 11 peptides. Score 0.382 Round 5: 129 peptides, 22 chains. Longest chain 11 peptides. Score 0.374 Taking the results from Round 4 Chains 20, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 6396 restraints for refining 2605 atoms. 6008 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2204 (Rfree = 0.000) for 2605 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 27: After refmac, R = 0.2217 (Rfree = 0.000) for 2581 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 28: After refmac, R = 0.2151 (Rfree = 0.000) for 2568 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 29: After refmac, R = 0.2204 (Rfree = 0.000) for 2557 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 30: After refmac, R = 0.2359 (Rfree = 0.000) for 2546 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.75 3.96 Search for helices and strands: 0 residues in 0 chains, 2639 seeds are put forward NCS extension: 9 residues added (1 deleted due to clashes), 2648 seeds are put forward Round 1: 113 peptides, 26 chains. Longest chain 7 peptides. Score 0.214 Round 2: 121 peptides, 24 chains. Longest chain 9 peptides. Score 0.296 Round 3: 132 peptides, 23 chains. Longest chain 10 peptides. Score 0.368 Round 4: 139 peptides, 23 chains. Longest chain 11 peptides. Score 0.399 Round 5: 130 peptides, 20 chains. Longest chain 11 peptides. Score 0.418 Taking the results from Round 5 Chains 20, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 6023 restraints for refining 2595 atoms. 5603 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2365 (Rfree = 0.000) for 2595 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 32: After refmac, R = 0.2264 (Rfree = 0.000) for 2583 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 33: After refmac, R = 0.1914 (Rfree = 0.000) for 2571 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 34: After refmac, R = 0.2202 (Rfree = 0.000) for 2563 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 35: After refmac, R = 0.2203 (Rfree = 0.000) for 2560 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.80 4.01 Search for helices and strands: 0 residues in 0 chains, 2635 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 2647 seeds are put forward Round 1: 119 peptides, 25 chains. Longest chain 8 peptides. Score 0.266 Round 2: 142 peptides, 26 chains. Longest chain 10 peptides. Score 0.355 Round 3: 155 peptides, 28 chains. Longest chain 12 peptides. Score 0.375 Round 4: 150 peptides, 27 chains. Longest chain 13 peptides. Score 0.372 Round 5: 157 peptides, 28 chains. Longest chain 13 peptides. Score 0.384 Taking the results from Round 5 Chains 28, Residues 129, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 6154 restraints for refining 2635 atoms. 5666 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2211 (Rfree = 0.000) for 2635 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 37: After refmac, R = 0.2076 (Rfree = 0.000) for 2612 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. Cycle 38: After refmac, R = 0.2022 (Rfree = 0.000) for 2595 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 39: After refmac, R = 0.1799 (Rfree = 0.000) for 2592 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 40: After refmac, R = 0.1945 (Rfree = 0.000) for 2588 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.72 3.92 Search for helices and strands: 0 residues in 0 chains, 2665 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2686 seeds are put forward Round 1: 93 peptides, 21 chains. Longest chain 6 peptides. Score 0.217 Round 2: 104 peptides, 21 chains. Longest chain 9 peptides. Score 0.275 Round 3: 107 peptides, 20 chains. Longest chain 8 peptides. Score 0.312 Round 4: 102 peptides, 18 chains. Longest chain 9 peptides. Score 0.330 Round 5: 105 peptides, 17 chains. Longest chain 9 peptides. Score 0.365 Taking the results from Round 5 Chains 17, Residues 88, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 6321 restraints for refining 2641 atoms. 5969 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2585 (Rfree = 0.000) for 2641 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. Cycle 42: After refmac, R = 0.2469 (Rfree = 0.000) for 2621 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 43: After refmac, R = 0.1754 (Rfree = 0.000) for 2610 atoms. Found 7 (12 requested) and removed 13 (6 requested) atoms. Cycle 44: After refmac, R = 0.2201 (Rfree = 0.000) for 2599 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 45: After refmac, R = 0.1731 (Rfree = 0.000) for 2595 atoms. Found 5 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.75 3.96 Search for helices and strands: 0 residues in 0 chains, 2643 seeds are put forward NCS extension: 0 residues added, 2643 seeds are put forward Round 1: 95 peptides, 22 chains. Longest chain 7 peptides. Score 0.206 Round 2: 104 peptides, 21 chains. Longest chain 12 peptides. Score 0.275 Round 3: 104 peptides, 20 chains. Longest chain 9 peptides. Score 0.297 Round 4: 94 peptides, 18 chains. Longest chain 9 peptides. Score 0.290 Round 5: 96 peptides, 18 chains. Longest chain 9 peptides. Score 0.300 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2opl-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3418 reflections ( 99.19 % complete ) and 6547 restraints for refining 2665 atoms. 6253 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2268 (Rfree = 0.000) for 2665 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2348 (Rfree = 0.000) for 2642 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2009 (Rfree = 0.000) for 2629 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1504 (Rfree = 0.000) for 2611 atoms. TimeTaking 30.72